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      A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA

      research-article
      1 , , 1 , 2 , 3 , 4 , 1 , 1 , 5 , 1 , 1 , 6 , 1 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 1 , 2 , 14 , 14 , 14 , 14 , 1 , 2 , 15 , 16 , 17 , 1 , 18 , 13 , 19 , PhyloNorway Consortium, 1 , 21 , 10 , 1 , 20 , 22 , 1 , 3 , 23 , 1 , 24 , 25 , 3 , 1 , 1 , 2 , 26 ,
      Nature
      Nature Publishing Group UK
      Molecular ecology, Evolutionary ecology, Ecological genetics, Evolutionary ecology

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          Abstract

          Late Pliocene and Early Pleistocene epochs 3.6 to 0.8 million years ago 1 had climates resembling those forecasted under future warming 2 . Palaeoclimatic records show strong polar amplification with mean annual temperatures of 11–19 °C above contemporary values 3, 4 . The biological communities inhabiting the Arctic during this time remain poorly known because fossils are rare 5 . Here we report an ancient environmental DNA 6 (eDNA) record describing the rich plant and animal assemblages of the Kap København Formation in North Greenland, dated to around two million years ago. The record shows an open boreal forest ecosystem with mixed vegetation of poplar, birch and thuja trees, as well as a variety of Arctic and boreal shrubs and herbs, many of which had not previously been detected at the site from macrofossil and pollen records. The DNA record confirms the presence of hare and mitochondrial DNA from animals including mastodons, reindeer, rodents and geese, all ancestral to their present-day and late Pleistocene relatives. The presence of marine species including horseshoe crab and green algae support a warmer climate than today. The reconstructed ecosystem has no modern analogue. The survival of such ancient eDNA probably relates to its binding to mineral surfaces. Our findings open new areas of genetic research, demonstrating that it is possible to track the ecology and evolution of biological communities from two million years ago using ancient eDNA.

          Abstract

          Analysis of two-million-year-old ancient environmental DNA from the Kap København Formation in North Greenland shows there was an open boreal forest with diverse plant and animal species, of which several taxa have not previously been detected at the site, representing an ecosystem that has no present-day analogue.

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          The Sequence Alignment/Map format and SAMtools

          Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
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            Fast gapped-read alignment with Bowtie 2.

            As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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              Fast and accurate short read alignment with Burrows–Wheeler transform

              Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: rd@sanger.ac.uk
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                Author and article information

                Contributors
                kurtk@sund.ku.dk
                ew482@cam.ac.uk
                Journal
                Nature
                Nature
                Nature
                Nature Publishing Group UK (London )
                0028-0836
                1476-4687
                7 December 2022
                7 December 2022
                2022
                : 612
                : 7939
                : 283-291
                Affiliations
                [1 ]GRID grid.5254.6, ISNI 0000 0001 0674 042X, Lundbeck Foundation GeoGenetics Centre, Globe Institute, , University of Copenhagen, ; Copenhagen, Denmark
                [2 ]GRID grid.5335.0, ISNI 0000000121885934, Department of Zoology, , University of Cambridge, ; Cambridge, UK
                [3 ]GRID grid.5335.0, ISNI 0000000121885934, Department of Genetics, , University of Cambridge, ; Cambridge, UK
                [4 ]Section for Molecular Ecology and Evolution, The Globe Institute, Faculty of Health and Medical Sciences, Copenhagen, Denmark
                [5 ]GRID grid.5254.6, ISNI 0000 0001 0674 042X, Niels Bohr Institute, , University of Copenhagen, ; Copenhagen, Denmark
                [6 ]GRID grid.461907.d, Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, IRD, Université Gustave Eiffel, ISTerre, ; Grenoble, France
                [7 ]Nordic Foundation for Development and Ecology (NORDECO), Copenhagen, Denmark
                [8 ]GRID grid.5254.6, ISNI 0000 0001 0674 042X, DIS Study Abroad in Scandinavia, , University of Copenhagen, ; Copenhagen, Denmark
                [9 ]GRID grid.13508.3f, ISNI 0000 0001 1017 5662, Department of Glaciology and Climate, , Geological Survey of Denmark and Greenland, ; Copenhagen, Denmark
                [10 ]GRID grid.4886.2, ISNI 0000 0001 2192 9124, Geological Institute, , Russian Academy of Sciences, ; Moscow, Russia
                [11 ]GRID grid.8993.b, ISNI 0000 0004 1936 9457, Department of Earth Sciences, , Uppsala University, ; Uppsala, Sweden
                [12 ]GRID grid.55602.34, ISNI 0000 0004 1936 8200, Department of Earth and Environmental Sciences, , Dalhousie University, ; Halifax, Nova Scotia Canada
                [13 ]GRID grid.10919.30, ISNI 0000000122595234, The Arctic University Museum of Norway, UiT—The Arctic University of Norway, ; Tromsø, Norway
                [14 ]GRID grid.418674.8, ISNI 0000 0004 0533 4528, Carlsberg Research Laboratory, ; Copenhagen, Denmark
                [15 ]GRID grid.4991.5, ISNI 0000 0004 1936 8948, Environmental Change Institute, School of Geography and the Environment, , University of Oxford, ; Oxford, UK
                [16 ]GRID grid.13508.3f, ISNI 0000 0001 1017 5662, Geological Survey of Denmark and Greenland, , (GEUS), ; Copenhagen, Denmark
                [17 ]GRID grid.13508.3f, ISNI 0000 0001 1017 5662, Department of Geophysics and Sedimentary Basins, , Geological Survey of Denmark and Greenland, ; Copenhagen, Denmark
                [18 ]GRID grid.1032.0, ISNI 0000 0004 0375 4078, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, , Curtin University, ; Perth, Western Australia Australia
                [19 ]GRID grid.462909.0, ISNI 0000 0004 0609 8934, University of Grenoble-Alpes, Université Savoie Mont Blanc, CNRS, LECA, ; Grenoble, France
                [20 ]GRID grid.4444.0, ISNI 0000 0001 2112 9282, Institut de Biologie de l’Ecole Normale Supérieure (IBENS), , Ecole Normale Supérieure, CNRS, INSERM Université PSL, ; Paris, France
                [21 ]GRID grid.10919.30, ISNI 0000000122595234, Department of Geosciences, , UiT—The Arctic University of Norway, ; Tromsø, Norway
                [22 ]GRID grid.4991.5, ISNI 0000 0004 1936 8948, School of Geography and the Environment, , University of Oxford, ; Oxford, UK
                [23 ]GRID grid.250008.f, ISNI 0000 0001 2160 9702, Center for Accelerator Mass Spectrometry, , Lawrence Livermore National Laboratory, ; Livermore, CA USA
                [24 ]GRID grid.5335.0, ISNI 0000000121885934, Department of Archaeology, , University of Cambridge, ; Cambridge, UK
                [25 ]GRID grid.5254.6, ISNI 0000 0001 0674 042X, Section for GeoBiology, Globe Institute, , University of Copenhagen, ; Copenhagen, Denmark
                [26 ]GRID grid.7704.4, ISNI 0000 0001 2297 4381, MARUM, , University of Bremen, ; Bremen, Germany
                Author information
                http://orcid.org/0000-0002-8871-5179
                http://orcid.org/0000-0002-7291-8887
                http://orcid.org/0000-0002-0648-4224
                http://orcid.org/0000-0002-6978-6633
                http://orcid.org/0000-0002-0720-7229
                http://orcid.org/0000-0001-7854-3724
                http://orcid.org/0000-0002-8557-5131
                http://orcid.org/0000-0002-0814-8574
                http://orcid.org/0000-0002-8610-1085
                http://orcid.org/0000-0002-7838-226X
                http://orcid.org/0000-0001-5923-3667
                http://orcid.org/0000-0001-6720-8832
                http://orcid.org/0000-0001-6503-0495
                http://orcid.org/0000-0001-7317-4376
                http://orcid.org/0000-0001-5459-6186
                http://orcid.org/0000-0001-7168-9405
                http://orcid.org/0000-0001-7507-6729
                http://orcid.org/0000-0001-5778-6620
                http://orcid.org/0000-0002-8679-490X
                http://orcid.org/0000-0003-3835-6187
                http://orcid.org/0000-0002-8438-2223
                http://orcid.org/0000-0003-2916-1425
                http://orcid.org/0000-0003-2818-8319
                http://orcid.org/0000-0002-9130-1006
                http://orcid.org/0000-0002-7081-6748
                Article
                5453
                10.1038/s41586-022-05453-y
                9729109
                36477129
                ad6fe141-30c5-4bb5-bfba-2abb55f5a304
                © The Author(s) 2022

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 30 September 2021
                : 18 October 2022
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                molecular ecology,evolutionary ecology,ecological genetics
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                molecular ecology, evolutionary ecology, ecological genetics

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